scholarly journals Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction

2018 ◽  
Vol 46 (12) ◽  
pp. 5875-5885 ◽  
Author(s):  
Jithesh Kottur ◽  
Deepak T Nair
Keyword(s):  
Dna Synthesis ◽  
Synthesis Reaction ◽  
Critical Step ◽  
Pyrophosphate Hydrolysis

scholarly journals A New Direct Single-Molecule Observation Method for DNA Synthesis Reaction Using Fluorescent Replication Protein A

Sensors ◽  
2014 ◽  
Vol 14 (3) ◽  
pp. 5174-5182 ◽  
Author(s):  
Shunsuke Takahashi ◽  
Shohei Kawasaki ◽  
Hidefumi Miyata ◽  
Hirofumi Kurita ◽  
Takeshi Mizuno ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Single Molecule ◽  
Protein A ◽  
Replication Protein A ◽  
Replication Protein ◽  
Synthesis Reaction ◽  
Observation Method

scholarly journals Repair of a synthetic abasic site in DNA in a Xenopus laevis oocyte extract.

1989 ◽  
Vol 9 (9) ◽  
pp. 3750-3757 ◽  
Author(s):  
Y Matsumoto ◽  
D F Bogenhagen
Keyword(s):  
Dna Damage ◽  
Xenopus Laevis ◽  
Dna Synthesis ◽  
Patch Repair ◽  
Synthetic Analog ◽  
Xenopus Laevis Oocyte ◽  
Synthesis Reaction ◽  
Abasic Site ◽  
Circular Dna ◽  
Circular Dnas

Covalently closed circular DNA containing a synthetic analog of an abasic site at a unique position was used as a substrate to study DNA repair. Incubation of this DNA in Xenopus laevis oocyte extracts resulted in rapid cleavage of the DNA at the abasic site by a class II apurinic-apyrimidinic endonuclease, followed by complete repair within 40 min. Nicked circular DNAs persisted for several minutes before repair by an ATP-dependent DNA synthesis reaction. The repair-related DNA synthesis was localized within 3 or 4 nucleotides surrounding the abasic site. These results are consistent with the short-patch repair reported for DNA damage at heterogeneous sites in human cells (J. D. Regan and R. B. Setlow, Cancer Res. 34:3318-3325, 1974).

Repair of a synthetic abasic site in DNA in a Xenopus laevis oocyte extract

1989 ◽  
Vol 9 (9) ◽  
pp. 3750-3757
Author(s):  
Y Matsumoto ◽  
D F Bogenhagen
Keyword(s):  
Dna Damage ◽  
Xenopus Laevis ◽  
Dna Synthesis ◽  
Patch Repair ◽  
Synthetic Analog ◽  
Xenopus Laevis Oocyte ◽  
Synthesis Reaction ◽  
Abasic Site ◽  
Circular Dna ◽  
Circular Dnas

Covalently closed circular DNA containing a synthetic analog of an abasic site at a unique position was used as a substrate to study DNA repair. Incubation of this DNA in Xenopus laevis oocyte extracts resulted in rapid cleavage of the DNA at the abasic site by a class II apurinic-apyrimidinic endonuclease, followed by complete repair within 40 min. Nicked circular DNAs persisted for several minutes before repair by an ATP-dependent DNA synthesis reaction. The repair-related DNA synthesis was localized within 3 or 4 nucleotides surrounding the abasic site. These results are consistent with the short-patch repair reported for DNA damage at heterogeneous sites in human cells (J. D. Regan and R. B. Setlow, Cancer Res. 34:3318-3325, 1974).

A directed nucleotide-sequencing approach for single-stranded vectors based on recloning intermediates of a progressive DNA synthesis reaction

Gene ◽  
1988 ◽  
Vol 67 (2) ◽  
pp. 159-168 ◽  
Author(s):  
Frank H. Burton ◽  
Daniel D. Loeb ◽  
Royal A. McGraw ◽  
Marshall H. Edgell ◽  
Clyde A. Hutchison
Keyword(s):  
Dna Synthesis ◽  
Nucleotide Sequencing ◽  
Synthesis Reaction

scholarly journals Multiple deprotonation paths of the nucleophile 3′-OH in the DNA synthesis reaction

2021 ◽  
Vol 118 (23) ◽  
pp. e2103990118
Author(s):  
Mark T. Gregory ◽  
Yang Gao ◽  
Qiang Cui ◽  
Wei Yang
Keyword(s):  
Dna Synthesis ◽  
Catalytic Efficiency ◽  
Synthesis Reaction ◽  
Site Mutation ◽  
Phosphodiester Bond ◽  
The Third ◽  
Human Dna ◽  
Steady State Kinetics ◽  
Dynamics Simulations ◽  
Deoxyribonucleoside Triphosphate

DNA synthesis by polymerases is essential for life. Deprotonation of the nucleophile 3′-OH is thought to be the obligatory first step in the DNA synthesis reaction. We have examined each entity surrounding the nucleophile 3′-OH in the reaction catalyzed by human DNA polymerase (Pol) η and delineated the deprotonation process by combining mutagenesis with steady-state kinetics, high-resolution structures of in crystallo reactions, and molecular dynamics simulations. The conserved S113 residue, which forms a hydrogen bond with the primer 3′-OH in the ground state, stabilizes the primer end in the active site. Mutation of S113 to alanine destabilizes primer binding and reduces the catalytic efficiency. Displacement of a water molecule that is hydrogen bonded to the 3′-OH using the 2′-OH of a ribonucleotide or 2′-F has little effect on catalysis. Moreover, combining the S113A mutation with 2′-F replacement, which removes two potential hydrogen acceptors of the 3′-OH, does not reduce the catalytic efficiency. We conclude that the proton can leave the O3′ via alternative paths, supporting the hypothesis that binding of the third Mg2+ initiates the reaction by breaking the α–β phosphodiester bond of an incoming deoxyribonucleoside triphosphate (dNTP).

Use of Antibody to aid Visualization of Protein at the Termini of Bacteriophage Ø29 DNA

1980 ◽  
Vol 38 ◽  
pp. 540-541
Author(s):  
Dwight Anderson ◽  
Charlene Peterson ◽  
Gursaran Notani ◽  
Bernard Reilly
Keyword(s):  
Electron Microscopy ◽  
Bacillus Subtilis ◽  
Dna Synthesis ◽  
Restriction Endonuclease ◽  
Protein Complex ◽  
Protein Product ◽  
Viral Dna ◽  
Small Proteins ◽  
Antibody Labeling ◽  
Subtilis Bacteriophage

The protein product of cistron 3 of Bacillus subtilis bacteriophage Ø29 is essential for viral DNA synthesis and is covalently bound to the 5’-termini of the Ø29 DNA. When the DNA-protein complex is cleaved with a restriction endonuclease, the protein is bound to the two terminal fragments. The 28,000 dalton protein can be visualized by electron microscopy as a small dot and often is seen only when two ends are in apposition as in multimers or in glutaraldehyde-fixed aggregates. We sought to improve the visibility of these small proteins by use of antibody labeling.

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